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Novel Picornavirus (Family Picornaviridae) from Freshwater Fishes

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Novel Picornavirus (Family Picornaviridae) from Freshwater Fishes Archives of Virology (2021) 166:2627–2632 https://doi.org/10.1007/s00705-021-05167-y ANNOTATED SEQUENCE RECORD Novel picornavirus (family Picornaviridae) from freshwater fshes (Perca fuviatilis, Sander lucioperca, and Ameiurus melas) in Hungary Renáta Hargitai1 · Péter Pankovics1 · Ákos Boros1 · Róbert Mátics2 · Eda Altan3 · Eric Delwart3,4 · Gábor Reuter1 Received: 1 March 2021 / Accepted: 21 May 2021 / Published online: 13 July 2021 © The Author(s) 2021 Abstract In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fuviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fsh species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5’UTR IRES-?/ NPG↓P H-box/NC VPg Pro Pol P1(VP0-VP3-VP1)/P2(2A1 -2A2 -2B-2C)/P3(3A-3B -3C -3D )/3’UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fsh- origin species in an unassigned genus in the family Picornaviridae. Introduction picornaviruses have also been identifed in lower vertebrates, including amphibians (newts) [16, 19], reptiles (tortoises) Picornaviruses are small non-enveloped viruses with a pos- [8, 15], and fsh. In the last group, six ofcial fsh-origin itive-sense, single-stranded RNA genome, belonging to the picornavirus genera – Limnipivirus from bluegill [4], carp family Picornaviridae. The family consists of 158 species [13], and minnow [18]; Potamipivirus from eel [9] and stick- grouped into 68 genera (https:// www. picor navir idae. com/ leback [12]; Fipivirus from sharpbelly, crossorhombus, jack index. html). Not only is the known genetic diversity of the mackerel, wrasse, and banjofsh [20]; Symapivirus from tri- picornaviruses expanding rapidly but the number of known plecross lizardfsh [20]; Rajidapivirus from sharpspine skate host species is also increasing. Picornaviruses have been [20], and Danipivirus from zebrafsh [1] – have been estab- identifed in a wide range of vertebrates from fsh to mam- lished and approved (https://talk. ictvo nline. org/ ictv- repor ts/ mals, including humans. Most of the known picornaviruses ictv_ online_ report/ posit ive- sense- rna- virus es/w/ picor navir were found in mammals and birds, but in recent years, novel idae.https://www. picor navir idae. com/ index. html ), although there are further unassigned picornaviruses that have been discovered in diferent fsh species [20]. Handling Editor: Kalpana Agnihotri. Some picornaviruses are important viral pathogens, caus- ing a wide range of diseases in humans and wild, domestic, Nucleotide sequence data reported are available in the DDBJ/ and laboratory animals. However, little is known about the EMBL/GenBank databases under the accession number MW590713. diversity, epidemiology, and disease-causing potential of fsh picornaviruses [14]. * Gábor Reuter In this study, we report the identifcation and complete [email protected] genome characterization of a potentially novel picornavirus Perca fuviatilis, Sander lucioperca 1 Department of Medical Microbiology and Immunology, in freshwater fshes ( , and Medical School, University of Pécs, Szigeti út 12., Ameiurus melas) in Hungary. 7624 Pecs, Hungary 2 Hungarian Nature Research Society, Ajka, Hungary 3 Vitalant Research Institute, San Francisco, CA, USA 4 University of California, San Francisco, CA, USA Vol.:(0123456789)1 3 2628 R. Hargitai et al. Materials and methods were tested individually by the RT-PCR method, using the PerchPV-screen2-F/R (Supplementary Table S2) screening A total of 62 faecal samples were collected directly from primer pair. 13 diferent freshwater fsh (Supplementary Table S1) Sequence alignments of the P1, 2C, and 3CD regions living in natural and artifcial open-air fshponds in the were done using GeneDoc (version 2.7) and the MUSCLE vicinity of Szarvas (Eastern Hungary) in the year 2015. web server based on the amino acid sequences of the studied The fsh showed no clinical signs of disease during sample fsh picornavirus and representative picornaviruses available collection and were released immediately after sampling. in the GenBank database. Phylogenetic analysis was per- A specimen pool containing faecal samples from three formed using MEGA X (version 10.2.3), creating maximum- European perch (M9, M13 and M15) were selected for likelihood trees using the substitution model LG+F+G+I viral metagenomics analysis. Briefly, 200 μl of PBS- for P1 and 3CD analysis and LG+G+I for 2C, with 1000 diluted specimen was passed through a 0.45-μm sterile bootstrap replicates as described previously [1]. Potential flter (Millipore) and centrifuged at 6,000 × g for 5 min. secondary RNA structures of the 5’ and 3’ UTRs of the The fltrate was then treated with a mixture of DNases and analyzed picornavirus sequences were predicted using Mfold RNases (Turbo DNase, Invitrogen; Baseline Zero DNase, software [22]. Epicentre Biotechnologies; Benzonase Nuclease, Nova- The nucleotide (nt) and amino acid (aa) sequences of gen; RNase A, Fermentas) at 37° C for 2 hours to digest European perch picornavirus (perchPV/M9/2015/HUN) unprotected nucleic acids [17]. Viral-particle-protected have been deposited in the GenBank database under the nucleic acids were extracted using a MagMAX Viral RNA accession number MW590713. Isolation Kit (Ambion, Austin, USA) with RNase inhibitor (RiboLock RNase Inhibitor, Fermentas) during the elution step. Sequence-independent random RT-PCR amplifca- Results tion [21] with 20 PCR cycles was used, and a viral cDNA library with 250 base-paired ends was constructed using A specimen pool containing three faecal samples from Euro- a Nextera XT DNA Library Preparation Kit (Illumina). pean perch was subjected to viral metagenomics analysis. The library was sequenced on an Illumina MiSeq platform After de novo assembly of the 16,612,456 sequence reads, according to the manufacturer’s instructions. The metagen- 58,855 reads from this pool were found to show similarity -10 omic reads were trimmed, assembled de novo [7], and ana- (BLASTx cutof E-value ≤ 10 ) to viral sequences. The lyzed using an in-house pipeline [17]. Briefy, the singlets sequences with more than 100 reads were from unclassifed and assembled contigs greater than 250 bp were compared viruses (n = 13,542), as well as the families Parvoviridae to the GenBank [6] protein database using BLASTx (ver- (n = 15,209), Dicistroviridae (n = 12,081), Reoviridae (n sion 2.2.7) [2], using an E-value cutof of 0.01. Candidate = 5,360), Picornaviridae (n = 3,198), Microviridae (n = viral hits were then compared to a non-viral non-redun- 2,689), Circoviridae (n = 1,825), Tombusviridae (n = 794), dant protein database to remove false positive viral hits. Permutotetraviridae (n = 643), Phycodnaviridae (n = 289), Virus-family-level categorization of all viral metagenomic Virgaviridae (n = 170), and Nanoviridae (n = 133). sequences was based on the best BLASTx scores (E-value Sequence reads/contigs corresponding to family Picor- ≤ 10-10). Metagenomic raw sequence read data are avail- naviridae were selected for further analysis. The longest able upon request. picornavirus contig was 3,423 nucleotides (nt) long, and A sequence-specifc screening primer pair (PerchPV- the encoded protein had only 40.2% aa sequence identity screen1-F/R, Supplementary Table S2) was designed for to the 2C/3C-3D region of eel picornavirus 1 strain F15/5 the 3D region to identify the viral genome of the study (NC_022332), a member of the species Potamipivirus A in strain from the specimen pool. The PCR thermocycler the genus Potamipivirus [9]. A sequence-specifc screening program consisted of 3 min at 95º C, 40 cycles for 30 primer pair was designed based on the 3D region of the s at 95º C, 20 s at 55º C, and 30 s at 72º C, and a fnal picornavirus sequence contig (Supplementary Table S2) to 3-min extension at 72º C using a C1000 Touch Thermal identify the picornavirus strain in the specimen pool. One Cycler (Bio-Rad). In addition, diferent sets of specifc of the three specimens from European perch was RT-PCR primers (Supplementary Table S2) were designed based positive, and this sample (M9) was selected for further study. on the sequences of the metagenomics reads/contigs and The complete genome – including the complete cod- the amplifed PCR products for the verifcation of the ing regions – of European perch picornavirus (perchPV/ metagenomics contig and to obtain the complete viral M9/2015/HUN, MW590713) is 7,741 nt long excluding the genome sequence, including the 5’ and 3’ ends, of the poly(A) tail (Fig. 1). The genome organization is as follows: IRES-?/ NPG↓P H-box/NC study strain (perchPV/M9/2015/HUN). All faecal samples 5’UTR P1(VP0-VP3-VP1)/P2(2A1 -2A2 - 2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3’UTR-poly(A). It has 1 3 Novel picornavirus from freshwater fshes 2629 Fig. 1 Schematic genome organization of perch picornavirus strain P4/P4’ cleavage sites are indicated above the genome map. Question perchPV/M9/2015/HUN (GenBank accession no. MW590713). The marks and dotted lines indicate the uncertain borders of VP3/VP1, genome map is drawn to scale. VP0, VP3, and VP1 represent viral VP1/2A1, and 2C/3A. The IRES type of the 5’UTR is unknown (see structural proteins and are shown in grey. Nucleotide (upper num- Fig. 2). aa, amino acid; nt, nucleotide; RdRp, RNA-dependent RNA ber) and amino acid (lower number) lengths are indicated in each polymerase; UTR, untranslated region; VP, viral protein gene box.
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